CropGF: a comprehensive visual platform for crop gene family mining and analysis

Xu, Jing; Zhu, Can; Su, M.; Li, Sida; Chao, Haoyu; Chen, Ming

doi:10.1093/database/baad051

Cited by 3 publications

(3 citation statements)

References 22 publications

(23 reference statements)

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“…Hence, we excluded it and renamed Os06g0527300 as OsCNGC3. This result is consistent with the recently published gene family visualization results [ 22 ]. We hypothesize that the reason for this phenomenon may be the different sources of the reference genome.…”

Section: Discussionsupporting

confidence: 94%

“…The phylogenetic tree was then embellished using the online mapping site iTOL (https://itol.embl.de/ (accessed on 26 September 2023)). The newly published gene family visualization website (https://bis.zju.edu.cn/cropgf/analysis/gene-info (accessed on 26 September 2023)) was used for heatmap visualization using Tbtools after downloading the expression data of OsCNGC genes in different tissues and under abiotic stresses [22,26].…”

Section: Phylogenetic Tree Construction and Gene Expression Specifici...mentioning

confidence: 99%

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Identification of the CNGC Gene Family in Rice and Mining of Alleles for Application in Rice Improvement

Wang,

Wu,

Zhang

et al. 2023

Plants

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Cyclic nucleotide-gated ion channel (CNGC) gene regulation plays important roles in plant immune and abiotic stress response. Here, we identified 16 CNGC genes in rice (Oryza sativa). Then, we analyzed their chromosomal location, physicochemical properties, subcellular localization, gene functional interaction network, cis-acting elements, phylogenetic relationships, collinearity, expression in tissues under normal conditions and abiotic stresses, and geng-cds-haplotype (gcHap) diversity in 3010 gcHaps. As a result, OsCNGC3 (Os06g0527300) was identified as a gene different from previous report, and OsCNGC genes were found to play important roles in rice population differentiation and rice improvement. Our results revealed their very strong differentiation between subspecies and populations, important roles in response to abiotic stresses, as well as strong genetic bottleneck effects and artificial selection of gcHap diversity in the modern breeding process of Xian (indica) and Geng (japonica) populations. The results also suggested that natural variations in most rice CNGC loci are potentially valuable for improving rice productivity and tolerance to abiotic stresses. The favorable alleles at the CNGC loci should be explored to facilitate their application in future rice improvement.

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Section: Discussionsupporting

confidence: 94%

Section: Phylogenetic Tree Construction and Gene Expression Specifici...mentioning

confidence: 99%

Identification of the CNGC Gene Family in Rice and Mining of Alleles for Application in Rice Improvement

Wang,

Wu,

Zhang

et al. 2023

Plants

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“…The detailed experimental methodology was described in Data file 6 (Table 1 ). We collaborated with Prof. Ming Chen of Zhejiang University to integrate the data of the L. apetalum genome into the CropGF platform ( https://bis.zju.edu.cn/cropgf/ ), which makes it very convenient to mine and analyze the L. apetalum gene family on this platform [ 15 ].…”

Section: Objectivementioning

confidence: 99%

A chromosome-level genome assembly and annotation of the medicinal plant Lepidium apetalum

Yan,

Zhu,

Jia

et al. 2024

BMC Genom Data

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Objectives As a traditional Chinese medicine, Lepidium apetalum is commonly used for purging the lung, relieving dyspnea, alleviating edema, and has the significant pharmacological effects on cardiovascular disease, hyperlipidemia, etc. In addition, the seeds of L. apetalum are rich in unsaturated fatty acids, sterols, glucosinolates and have a variety of biological activity compounds. To facilitate genomics, phylogenetic and secondary metabolite biosynthesis studies of L. apetalum, we assembled the high-resolution genome of L. apetalum. Data description We completed chromosome-level genome assembly of the L. apetalum genome (2n = 32), using Illumina HiSeq and PacBio Sequel sequencing platform as well as high-throughput chromosome conformation capture (Hi-C) technique. The assembled genome was 296.80 Mb in size, 34.41% in GC content, and 23.89% in repeated sequence content, including 316 contigs with a contig N50 of 16.31 Mb. Hi-C scaffolding resulted in 16 chromosomes occupying 99.79% of the assembled genome sequences. A total of 46 584 genes and 105 pseudogenes were predicted, 98.37% of which can be annotated to Nr, GO, KEGG, TrEMBL, SwissPort, Pfam and KOG databases. The high-quality reference genome generated by this study will provide accurate genetic information for the molecular biology research of L. apetalum.

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Quantitative phosphoproteomics reveals molecular pathway network in wheat resistance to stripe rust

Gan,

Tang,

et al. 2024

Stress Biology

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Protein phosphorylation plays an important role in immune signaling transduction in plant resistance to pathogens. Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), severely devastates wheat production. Nonetheless, the molecular mechanism of wheat resistance to stripe rust remains limited. In this study, quantitative phosphoproteomics was employed to investigate the protein phosphorylation changes in wheat challenged by Pst. A total of 1537 and 2470 differentially accumulated phosphoproteins (DAPs) were identified from four early infection stage (6, 12, 18 and 24 h post-inoculation) in incompatible and compatible wheat-Pst interactions respectively. KEGG analysis revealed that Oxidative Phosphorylation, Phosphatidylinositol Signaling, and MAPK signaling processes are distinctively enriched in incompatible interaction, while Biosynthesis of secondary metabolites and RNA degradation process were significantly enriched in compatible interactions. In particular, abundant changes in phosphorylation levels of chloroplast proteins were identified, suggesting the regulatory role of photosynthesis in wheat-Pst interaction, which is further emphasized by protein-protein interaction (PPI) network analysis. Motif-x analysis identified [xxxxSPxxxx] motif, likely phosphorylation sites for defensive response-related kinases, and a new [xxxxSSxxxx] motif significantly enriched in incompatible interaction. The results shed light on the early phosphorylation events contributing to wheat resistance against Pst. Moreover, our study demonstrated that the phosphorylation levels of Nucleoside diphosphate kinase TaNAPK1 are upregulated at 12 hpi with CYR23 and at 24 hpi with CYR31. Transient silencing of TaNAPK1 was able to attenuate wheat resistance to CYR23 and CYR31. Our study provides new insights into the mechanisms underlying Pst-wheat interactions and may provide database to find potential targets for the development of new resistant varieties.

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CropGF: a comprehensive visual platform for crop gene family mining and analysis

Cited by 3 publications

References 22 publications

Identification of the CNGC Gene Family in Rice and Mining of Alleles for Application in Rice Improvement

Identification of the CNGC Gene Family in Rice and Mining of Alleles for Application in Rice Improvement

A chromosome-level genome assembly and annotation of the medicinal plant Lepidium apetalum

Quantitative phosphoproteomics reveals molecular pathway network in wheat resistance to stripe rust

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